Background: In orthodontic treatment for bimaxillary protrusion, tooth extraction is often required. This study analyzed tooth displacement trends and stress distribution during clear aligner therapy in normal-root and short-root groups. Methods: Three-dimensional finite element models (FEMs) were constructed. The normal-root group had maxillary central incisors with 14 mm root lengths, whereas the short-root group had 7.6 mm root lengths. Both groups had 10 mm crown lengths. Three movement conditions were simulated: including C1: overall retraction of the maxillary anterior teeth by 0.2 mm; C2: distal movement of the maxillary canines to 1/3 of the extraction space, followed by 0.2 mm retraction of the maxillary central incisors; and C3: complete distal movement of the maxillary canines prior to 0.2 mm retraction of the maxillary central incisors. Molars served as anchorage units. Results: The maxillary central incisors showed the lowest von Mises stress and hydrostatic pressure under condition C1. Condition C2, in contrast, resulted in the highest hydrostatic pressure. Across all conditions, stress concentration was consistently found in the cervical regions of both the anterior and anchorage teeth. Under C1, displacement in both the X-axis (mesiodistal) and Z-axis (vertical) directions was the largest, indicating a stronger tendency for mesial crown movement and intrusive displacement of the teeth. Under C1, von Mises stress of the root was the highest, while hydrostatic stress was the lowest. Conclusions: Compared to the normal-root group, the short-rooted anterior teeth responded more favorably to overall retraction (C1). However, enhanced posterior anchorage is essential to manage the increased stress in these cases.